Acknowledgement

Data Provider

  • Cotton Genome Project, Beijing Genome Institute (BGI) & Institute of Cotton Research of CAAS

    The original data provider of Gossypium arboreum (A2) genome assembly/gene annotations Li F, Fan G, Wang K, et al. Genome sequence of the cultivated cotton Gossypium arboreum [J]. Nat Genet, 2014, 46(6): 567-572..

  • Joint Genome Institute (JGI)

    The original data provider of Gossypium raimondii (D5) genome assembly/gene annotations Paterson A H, Wendel J F, Gundlach H, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres [J]. Nature, 2012, 492(7429): 423-427..
    Data provider of 21 plant species genome.

  • Nanjing Agricultural Univerisity (NAU)

    The original data provider of Gossypium hirsutum (AD1) Zhang T, Hu Y, Jiang W, et al. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement [J]. Nat Biotechnol, 2015, 33(5): 531-537. and Gossypium barbadense (AD2) Liu X, Zhao B, Zheng H-J, et al. Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites [J]. Scientific Reports, 2015, 5: genome assembly/gene annotations.

  • Sequence Read Archive (SRA) in NCBI

    Data provider of RNA-seq data for all cotton species Kodama Y, Shumway M, Leinonen R. The Sequence Read Archive: explosive growth of sequencing data [J]. Nucleic Acids Res, 2012, 40(D1): D54-D56.

  • UniProt Knowledgebase/Swiss-Prot

    A comprehensive, high-quality and freely accessible resource of protein sequence and functional information Consortium T U. UniProt: a hub for protein information [J]. Nucleic Acids Res, 2015, 43(D1): D204-D212.. Used to define the names/descriptions of cotton genes

Data Analysis Software

  • Basic Local Alignment Search Tool (BLAST)

    A popular homology search tools to identify gene homology Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications [J]. BMC Bioinformatics, 2009, 10: 421.. Currently the intergrated data in this website are analyzed with BLAST+ v2.2.31.

  • InterProScan

    Predict protein domains and associated Gene Ontology (GO) and InterPro items Quevillon E, Silventoinen V, Pillai S, et al. InterProScan: protein domains identifier [J]. Nucleic Acids Res, 2005, 33(suppl 2): W116-W120.. Currently the intergrated data in this website are analyzed with InterProScan v5.16-55.0

  • KEGG Automatic Annotation Server

    Predict KEGG Orthology (KO) assignment for each gene and then related to its possible KEGG pathways Moriya Y, Itoh M, Okuda S, et al. KAAS: an automatic genome annotation and pathway reconstruction server [J]. Nucleic Acids Res, 2007, 35(suppl 2): W182-W185. . Currently the intergrated data in this website are analyzed with server access from 2015-11 to 2016-04

  • NGS QC Toolkit

    A toolkit for the quality control (QC) of next generation sequencing (NGS) data Patel R K, Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data [J]. PloS one, 2012, 7(2): e30619.. Currently the intergrated data in this website are analyzed with NGS QC Toolkit v2.3.3

  • Trimmomatic

    A flexible read trimming tool for Illumina NGS data Bolger A M, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data [J]. Bioinformatics, 2014: btu170.. Currently the intergrated data in this website are analyzed with Trimmomatic v0.3.3

  • TopHat

    A splice junction mapper for RNA-seq reads Kim D, Pertea G, Trapnell C, et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions [J]. Genome Biology, 2013, 14(4): . Currently the intergrated data in this website are analyzed with TopHat v2.1.1

  • Cufflinks

    Estimate expression levels (FPKM) and analysis differential expression for RNA-seq reads Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks [J]. Nature protocols, 2012, 7(3): 562-578.. Currently the intergrated data in this website are analyzed with Cufflinks v2.2.1

  • Bedtools

    Analysis short reads coverage across reference genomes and then used to visualize expression level on certain genome locus Quinlan A R, Hall I M. BEDTools: a flexible suite of utilities for comparing genomic features [J]. Bioinformatics, 2010, 26(6): 841-842.. Currently the intergrated data in this website are analyzed with Bedtools v2.25.0

  • R

    Use Fisher's Exact Test and Multi-Comparison to assess P-values of differential expression or enrichment items R: A language and environment for statistical computing. [http://www.r-project.org/]. Currently the intergrated data in this website are analyzed with R v3.3.0

  • EMBOSS

    Calculate several protein statistics values (Residue Composition, Molecular Weight, Charge, Isoelectric Point, ...);
    Search for restrict enzyme sites in genomes Rice P, Longden I, Bleasby A J. EMBOSS: The European Molecular Biology Open Software Suite [J]. Trends Genet, 2000, 16(6): 276-277..
    Currently the intergrated data in this website are analyzed with EMBOSS v6.5.7.0

  • BioPerl

    Calculate the Grand Average of Hydropathy value for proteins Stajich J E, Block D, Boulez K, et al. The Bioperl Toolkit: Perl Modules for the Life Sciences [J]. Genome Res, 2002, 12(10): 1611-1618.. Currently the intergrated data in this website are analyzed with BioPerl v1.6.924

  • RepeatMasker

    Search, categorize and mask repeat elements in genomes RepeatMasker Open-4.0 [http://www.repeatmasker.org]. Currently the intergrated data in this website are analyzed with RepeatMasker v4.0.5

  • BLAST-like alignment tool (BLAT)

    Map EST/CDS sequences to reference genomes Kent W J. BLAT - The BLAST-Like Alignment Tool [J]. Genome Res, 2002, 12(4): 656-664.. Currently the intergrated data in this website are analyzed with BLAT v.36x1

  • MAFFT

    A multiple sequence alignment tool to generate protein sequence alignments for ortholog groups Katoh K, Misawa K, Kuma K, et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform [J]. Nucleic Acids Res, 2002, 30(14): 3059-3066.. Currently the intergrated data in this website are analyzed with MAFFT v7.245

Website Framework

  • Bootstrap

    The front-end framework of this database. Intergrated with HTML, CSS, javascript tools and web fonts (Glyphicons/Font Awesome) it generates flexible page view on all kinds of devices: PC, tablet and mobile phones.

  • MySQL

    The database back-end for data storage and fetch.

  • PHP

    A script language used to fetch data from back-end databases and dynamically generate results on front-end web page.

Visualization Tools

  • JBrowse

    A genome browser to view gene locus, transcript, repeat elements, restrict enzyme sites, EST mapping, RNA-seq reads coverage, ..., in genomes Skinner M E, Uzilov A V, Stein L, et al. JBrowse: A next-generation genome browser [J]. Genome Res, 2009, 19(9): 1630-1638..
    Currently this website includes JBrowse v1.12.1
    In addition, the following third-party JBrowse plugins are used to extend data visualization:

  • SequenceServer

    A fast and modern BLAST+ web front-end server Priyam A, Woodcroft B J, Rai V, et al. Sequenceserver: a modern graphical user interface for custom BLAST databases [J]. Biorxiv, 2015: 033142.. Currently this website includes SequenceServer v1.0.5

  • Highcharts

    Generate interactive statistical charts (line charts, column charts, pie charts, heatmap charts,..., etc) on web pages. Currently this website includes Highcharts v4.2.0

  • Bootstrap Table

    An extended table tool with sort, pagination, export, and other added features. Currently this website includes Bootstrap Table v1.10.1

  • BioJS

    An open-source library of JavaScript components to visualise biological data Corpas M, Jimenez R, Carbon S J, et al. BioJS: an open source standard for biological visualisation–its status in 2014 [J]. F1000Research, 2014, 3: . Including the following components:

    • FeatureViewer (v0.1.34): visualization of position-based annotations in protein sequences. (e.g. protein domains)
    • Sequence-viewer (v0.2.17): visualization of DNA/protein sequences
    • MSA (v1.0.3): Display multiple sequence alignments

  • AmiGO

    Visualize the relationship of Gene Ontology (GO) items. Carbon S, Ireland A, Mungall C J, et al. AmiGO: online access to ontology and annotation data [J]. Bioinformatics, 2009, 25(2): 288-289.. Currently this website directly links to official AmiGO service in GO visualization.

References